Of course we'll kill all the Reapers. However, I also say this:
Depending on your choices through ME1-3, the end of ME3 will end in one of two ways (IMHO) (Well, of course not two ways, but I'll just say the polar opposites in the form of Dungeons and Dragons morality):
1. Lawful Good: The Reapers are extinct, the Citadel races (Asari, Turian, Salarian, Volus, Elcor, Hanar, Drell, Quarian) are all happy fun times with each other. More of the species are Council races now- like the Volus, since they whine so much and the part they'll play in funding the Unified Defense force. The recognized races (Vorcha, Batarian, and new ones which will apparently show up in ME3) also join up with the expanded Citadel friendliness. Cerberus is no more. The Krogan are led by Urdnot Wrex, and are achieving real cultural benefit so they are not Orcish anymore, and no longer a galactic threat. The Geth are apologized to, and become a Citadel race. For their selfless sacrifices during the defense of Earth and other planets, the Rachni become Citadel-accepted too. However, the cost is the extinction of Humanity. They were too selfless and cared more for galactic peace than their own survival.
2. Chaotic Evil: The Geth are extinct, they made their superstructure they talked about in ME2 through the Legion platform, which was kinda like a Death Star, but it got blown up while trying to defend the Quarians, who didn't accept them and so Reapers blew it up from one side where the Quarians blew it up from the other. The Thorian is back, and if you ACTUALLY READ every planet's description in ME1, the Batarians found a billion year old dead living ship. It was the Thorian's make! The Thorian was the first sentient species in the galaxy but over time it absorbed too much tech and bio-mass from other species and became the Reapers. It was true what Sovereign said- no one built them. Humanity survived, but no other race has enough genetic diversity to survive for long- and Humanity only has as many members as it does because they sacrificed EVERYONE else. Basically, the end of this version of ME3 is the same as the Protheans- they survived the galactic genocide, but died anyway. This time, however, there is no Reaper threat for the next group of species that evolves somewhere in the galaxy... they'll be safe.
In relation to how we kill the Reapers- Think of something no one said in this thread yet- the debris field on the other side of the Relay.
Each galactic genocide, it alluded that the highest tech is lower and lower, since it is based on that of the species before. The Protheans got some of that time back to us, to counteract it. But if that dead "living ship" meant anything, then there's something at least 37,000,000 years old if not a billion (the derelict is 37m) and finding tech from that forgotten civilization will really really help. Plus if I'm right on the Reapers being a child race of the Thorian, then we need to mass-produce Anti-Thorian gas and deliver it through melee- just Genophage-up the gas, tweak the DNA of the Rachni, and have their acid-spray decay the Reaper's organic parts. I mean, look at what EDI said, 'apparently, Reapers' looks are based on the organic race used to create them', and they do not look Prothean. They look Thorian.
We don't need to worry about the politics anymore, I think. You're Aria's friend (if you don't give hope to the Patriarch and you do point out people against Aria to her), Salarian friend (if you save both ranked Salarians at Saren's base and save the council), Turian friend (get the League of One medallions and save the Council), Asari friend (save the council, 'good' responses to the Consort), a respected Spectre (if you saved the council), ally of the Krogan (if Wrex leads), respected by the Quarians (max paragon through Tali's loyalty mission), Geth friend (Legion loyalty), Rachni friend (save them), and your girlfriend is the Shadow Broker (if you seduced and stayed loyal to Liara and got the DLC). The big unknowns to me are Conrad Verner (I think he only represents how the galaxy sees you, really) and Morinth, if you let her live, and the debris field past the Omega 6 Relay.